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JJ Dennehy CV Queens College of The City University of New York John J. The Graduate Center of The City University of New York [email protected] https://dennehylab.org Dennehy @DrJDennehy Education 1997–2003 PhD, Clark University, Biology 1995–1997 MA, University of Idaho, Zoology 1991–1995 BA, Merrimack College, Biology Academic Appointments 2018–Pres. Professor, Queens College CUNY 2013–2018 Associate Professor, Queens College CUNY 2007–2013 Assistant Professor, Queens College CUNY 2006–2007 Postdoctoral Associate, University at Albany SUNY 2003–2006 NSF Postdoctoral Fellow, Yale University External Funding 2021 National Science Foundation — Collaborative Research: HSI Pilot Planning Project: Enhancing STEM Education and Building Community for First Generation Students and/or Hispanic/Latinx Students Enhancing STEM (Co-PI, Submitted). 2020 Department of the Army — Materiel Command: Application of a High-Resolution Mass Spectrometer and Liquid Chromatograph to Chemical, Biological, And Neuroscience Research at Queens College (Co-PI, Submitted). Department of the Army — Materiel Command: Confocal Imaging to Identify Molecular Mechanisms of Biological Adaptation (Co-PI, Submitted). National Institutes of Health National Institute of Allergy and Infectious Diseases Award #1R21AI156798 — Novel Strategies for Treating Biofilm-Forming Pathogens with Phage Therapy (PI, $423,500). QIAGEN: NGS Research Grant Award — Phylodynamics of SARS-CoV-2 Isolated from NYC Wastewater (PI, $20,000). NSF Division of Environmental Biology Award #2032634 — RAPID: Collaborative Research: Metapopulation Modeling to Develop Strategies to Reduce COVID-19 Transmission in Public Spaces (PI, $200,000). New York City Department of Environmental Protection Project #17-2273 — Phylogenomic and Socioeconomic Correlates of COVID-19 Transmission in NYC (PI, $357,255). 2017 National Institutes of Health National Institute of General Medical Sciences Award #1R01GM124446 — Consequences and Control of Randomness in the Timing of Intracellular Events (Co-PI, $430,004). 2012 National Science Foundation Faculty Early Career Award #1148879 — CAREER: Population Dynamics and Evolutionary Ecology of Virus Emergence (PI, $713,900). 2009 National Science Foundation Division of Molecular and Cellular Biosciences Award #0918199 — Genetic and Molecular Basis of Bacteriophage Life History Variation (PI, $174,155). 2009 National Science Foundation Division of Environmental Biology Award #0804039 Research Assistantships for High School Students Supplement (PI, $17,848). 2008 Howard Hughes Medical Institute, Science Education Alliance, SEA PHAGES program 2008 National Science Foundation Division of Environmental Biology Award #0804039 — Population Dynamics and Evolution of Emerging Viruses (PI, $50,000). 2003 National Science Foundation Division of Biological Infrastructure Award #0310205 — Adaptive Landscapes and the Evolution of Cooperation in RNA Viruses (PI, $160,000). Publications (View in Google Scholar, ORCID iD) 41. Smyth DS, Trujillo M, UCheung K, UGao A, DHoxie I, Kannoly S, UKubota K, UMarkman M, MSan KM, USompanya G & Dennehy JJ. 2021. Detection of mutations associated with variants of concern via high throughput sequencing of SARS-CoV-2 isolated from NYC Wastewater medRxiv. (Submitted to mSphere). 40. DHoxie I & Dennehy JJ. 2021. Rotavirus A genome segments show distinct segregation and codon usage patterns. bioRxiv. (Submitted to Viruses MDPI). 39. Trujillo M, UCheung K, UGao A, DHoxie I, Kannoly S, UKubota N, MSan KM, Smyth DS & Dennehy JJ. 2021. Protocol for safe, affordable, and reproducible isolation and quantitation of SARS- CoV-2 RNA from wastewater. medRxiv. (Submitted to PLoS Protocols). 38. Kannoly S, Singh A & Dennehy JJ. 2021. An optimal lysis time maximizes bacteriophage fitness in quasi-continuous culture. bioRxiv. (In revision at mBio). 37. Pecson BM, Darby E, Haas CN, Amha Y, Bartolo M, Danielson R, Dearborn Y, Di Giovanni G, Ferguson C, Fevig S, Gaddis E, Gray D, Lukasik G, Mull B, Olivas L, Olivieri A, Qu Y, SARS-CoV-2 Interlaboratory Consortium. 2021. Reproducibility and sensitivity of 36 methods to quantify the SARS-CoV-2 genetic signal in raw wastewater: findings from an interlaboratory methods evaluation in the U.S. Environmental Science: Water Research & Technology. 36. Dunning-Hotopp JC, Baltrus DA, Bruno VM, Dennehy JJ, Gill SR, Maresca JA, Matthijnssens J, Newton ILG, Putonti C, Rasko DA, Rokas A, Roux S, Stajich JE. Stedman KM, Stewart FJ, & Thrash JC. 2020. Best practices for successfully writing and publishing a genome announcement in Microbial Resource Announcements. Microbiology Resource Announcements. 35. Kannoly S, UGao T, Dey S, Wang I-N, Singh A & Dennehy JJ. 2020. Optimum threshold minimizes noise in timing of intracellular events. iScience. 34. DHoxie I & Dennehy JJ. 2020. Intragenic recombination influences rotavirus diversity and evolution. Virus Evolution. 33. Baltrus DA, Cuomo CA, Dennehy JJ, Dunning-Hotopp JC, Maresca JA, Newton ILG, Rasko D, Rokas A, Roux S & Stajich JE. 2019. Future-proofing your Microbiology Resource Announcements genome assembly for reproducibility and clarity. Microbiology Resource Announcements. 32. DGhusinga K, Dennehy JJ & Singh A. 2017. First-passage time approach to controlling noise in timing of intra-cellular events. Proceedings of the National Academy of Sciences USA. 31. Dennehy JJ. 2016. Evolutionary ecology of virus emergence. Annals of the New York Academy of Sciences: The Year in Evolutionary Biology. 30. MEsposito LA, UGupta S, UPrasad A, UStreiter F & Dennehy JJ. 2016. Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias. Microbial Genomics. 29. DAhmadi M, Torshizi MAK, Rahimi S & Dennehy JJ. 2016. Prophylactic bacteriophage administration more effective than post-infection administration in reducing Salmonella enteritidis shedding in quails. Frontiers in Microbiology. 28. Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA PHAGES), Phage Hunters Integrating Research and Education (PHIRE), Mycobacterial Genetics Course (MGC), Cresawn SG, Jacobs WR Jr, Hendrix RW, Lawrence JG & Hatfull GF. 2015. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. eLife. 27. DFord BE, USun B, DCarpino J, UChapler ES, UChing J, UChoi Y, UJhun K, UKim JD, ULallos GG, UMorgenstern R, USingh S, UTheja S & Dennehy JJ. 2014. Frequency and fitness consequences of bacteriophage φ6 host range mutations. PLoS ONE. 26. Dennehy JJ. 2014. What ecologists can tell virologists. Annual Review of Microbiology. 25. Singh A & Dennehy JJ. 2014. Stochastic holin expression can account for lysis time variation in the bacteriophage λ. Journal of the Royal Society Interface. 24. Jordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ, Dennehy JJ, Denver DR, Dunbar D, Elgin SCR, Findley AM, Gissendanner CR, Golebiewska UP, Guild N, Hartzog GA, Grillo WH, Hollowell GP, Hughes LE, Johnson A, King RA, Lewis LO, Li W, Rosenzweig F, Rubin MR, Saha MS, Sandoz J, Shaffer CD, Taylor B, Temple T, Vazquez E, Ware VC, Barker LP, Bradley KW, Jacobs-Sera D, Pope WH, Russell DA, Cresawn SG, Lopatto D, Bailey CB & Hatfull, GF. 2014. A broadly implementable research course for first-year undergraduate students. mBio. 23. Hatfull GF, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) Program, KwaZulu-Natal Research Institute for Tuberculosis and HIV (K- RITH) Mycobacterial Genetics Course, University of California Los Angeles Research Immersion Laboratory in Virology, Phage Hunters Integrating Research and Education (PHIRE) program. (2013). The complete genome sequences of 63 mycobacteriophages. Genome Announcements. 22. Dennehy JJ, DDuffy S, O'Keefe KJ, Edwards SV & Turner PE. 2013. Frequent coinfection reduces RNA virus population genetic diversity. Journal of Heredity. 21. Dennehy JJ. 2012. What can bacteriophages tell us about host-parasite coevolution? International Journal of Evolutionary Biology. 20. Hatfull GF, Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Program, the KwaZulu-Natal Research Institute for Tuberculosis and HIV Mycobacterial Genetics Course Students, and the Phage Hunters Integrating Research and Education Program. 2012. The complete genome sequences of 138 mycobacteriophages. Journal of Virology. 19. UChing J, UMusheyev SA, HChowdhury D, HKim JA, UChoi Y & Dennehy JJ. 2012. Migration enhances adaptation in bacteriophage populations evolving in ecological sinks. Evolution. 18. ULi J & Dennehy JJ. 2011. Differential bacteriophage mortality on exposure to copper. Applied and Environmental Microbiology. 17. Dennehy JJ & Wang I-N. 2011. Factors influencing lysis time stochasticity in bacteriophage λ. BMC Microbiology. 16. Dennehy JJ, Friedenberg NA, McBride RC, Holt RD & Turner PE. 2010. Experimental evidence that source genetic variation drives pathogen emergence. Proceedings of the Royal Society, B - Biological Sciences. 15. DKhatchikian CE, Dennehy JJ, Vitek CJ & Livdahl TP. 2010. Environmental effects on bet hedging in Aedes mosquito egg hatch. Evolutionary Ecology. 14. Marshall JC, UButtars PR, UCallahan T, Dennehy JJ, DHarris DJ, ULunt B & UShupe R. 2009. In the academic job market, will you be competitive? A case study in ecology and evolutionary biology. Israel Journal of Ecology & Evolution. 13. Dennehy JJ. 2009. Bacteriophages
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